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  • Timinskas K, Kazlauskas D, Timinskas A, Venclovas Č. (2026) Diversity and distribution of bacterial DNA polymerases. Nucleic Acids Research, 54(4):gkag133. doi: 10.1093/nar/gkag133 [PubMed]
  • Jurgelaitis E, Zagorskaitė E, Kopūstas A, Ašmontas S, Manakova E, Dalgėdienė I, Tylenytė U, Šilanskas A, Toliušis P, Grybauskas A, Tutkus M, Venclovas Č, Zaremba M. (2025) Activation of the SPARDA defense system by filament assembly using a beta-relay signaling mechanism widespread in prokaryotic Argonautes. Cell Research, 35(12):1056–1078. doi: 10.1038/s41422-025-01198-1 [PubMed]
  • Makarova KS, Shmakov SA, Wolf YI, Mutz P, Altae-Tran H, Beisel CL, Brouns SJJ, Charpentier E, Cheng D, Doudna J, Haft DH, Horvath P, Moineau S, Mojica FJM, Pausch P, Pinilla-Redondo R, Shah SA, Šikšnys V, Terns MP, Tordoff J, Venclovas Č, White MF, Yakunin AF, Zhang F, Garrett RA, Backofen R, van der Oost J, Barrangou R, Koonin EV. (2025) An updated evolutionary classification of CRISPR–Cas systems including rare variants. Nature Microbiology, 10(12):3346–3361. doi: 10.1038/s41564-025-02180-8 [PubMed]
  • Dapkūnas J, Venclovas Č. (2025) Databases and web-based tools for studying structures of protein-nucleic acid complexes. Current Opinion in Structural Biology, 94:103079. doi: 10.1016/j.sbi.2025.103079 [PubMed]
  • Olechnovič K, Banciul R, Dapkūnas J, Venclovas Č. (2025) FTDMP: A framework for protein–protein, protein–DNA, and protein–RNA docking and scoring. Proteins. doi: 10.1002/prot.26792 [PubMed]
  • Dapkūnas J, Timinskas A, Olechnovič K, Tomkuvienė M, Venclovas Č. (2024) PPI3D: A web server for searching, analyzing and modeling protein–protein, protein–peptide and protein–nucleic acid interactions. Nucleic Acids Research, 52(W1):W264–W271. doi: 10.1093/nar/gkae278 [PubMed]
  • Mogila I, Tamulaitienė G, Keda K, Timinskas A, Rukšėnaitė A, Sasnauskas G, Venclovas Č, Šikšnys V, Tamulaitis G. (2023) Ribosomal stalk-captured CARF-RelE ribonuclease inhibits translation following CRISPR signaling. Science, 382(6674):1036–1041. doi: 10.1126/science.adj2107 [PubMed]
  • Olechnovič K, Venclovas Č. (2023) VoroIF-GNN: Voronoi tessellation-derived protein–protein interface assessment using a graph neural network. Proteins, 91(12):1879–1888. doi: 10.1002/prot.26554 [PubMed]
  • Olechnovič K, Valančauskas L, Dapkūnas J, Venclovas Č. (2023) Prediction of protein assemblies by structure sampling followed by interface-focused scoring. Proteins, 91(12):1724–1733. doi: 10.1002/prot.26569 [PubMed]
  • Sasnauskas G, Tamulaitienė G, Druteika G, Carabias A, Šilanskas A, Kazlauskas D, Venclovas Č, Montoya G, Karvelis T, Šikšnys V. (2023) TnpB structure reveals the minimal functional core of the Cas12 nuclease family. Nature, 616:384–389. doi: 10.1038/s41586-023-05826-x [PubMed]
  • Zaremba M, Dakinevičienė D, Golovinas E, Zagorskaitė E, Stankūnas E, Lopatina A, Sorek R, Manakova E, Rukšėnaitė A, Šilanskas A, Ašmontas S, Grybauskas A, Tylenytė U, Jurgelaitis E, Grigaitis R, Timinskas K, Venclovas Č, Šikšnys V. (2022) Short prokaryotic Argonautes provide defence against incoming mobile genetic elements through NAD+ depletion. Nature Microbiology, 7(11):1857–1869. doi: 10.1038/s41564-022-01239-0 [PubMed]
  • Olechnovič K, Venclovas Č. (2021) VoroContacts: A tool for the analysis of interatomic contacts in macromolecular structures. Bioinformatics, 37(24):4873–4875. doi: 10.1093/bioinformatics/btab448 [PubMed]
  • Dapkūnas J, Olechnovič K, Venclovas Č. (2021) Modeling of protein complexes in CASP14 with emphasis on the interaction interface prediction. Proteins, 89(12):1834–1843. doi: 10.1002/prot.26167 [PubMed]
  • Karvelis T, Druteika G, Bigelytė G, Budrė K, Žedaveinytė R, Šilanskas A, Kazlauskas D, Venclovas Č, Šikšnys V. (2021) Transposon-associated TnpB is a programmable RNA-guided DNA endonuclease. Nature, 599:692–696. doi: 10.1038/s41586-021-04058-1 [PubMed]
  • Gasiūnas G, Young JK, Karvelis T, Kazlauskas D, Urbaitis T, Jasnauskaitė M, Grušytė MM, Paulraj S, Wang PH, Hou Z, Dooley SK, Cigan M, Alarcon C, Chilcoat ND, Bigelytė G, Curcuru JL, Mabuchi M, Sun Z, Fuchs RT, Schildkraut E, Weigele PR, Jack WE, Robb GB, Venclovas Č, Šikšnys V. (2020) A catalogue of biochemically diverse CRISPR-Cas9 orthologs. Nature Communications, 11:5512. doi: 10.1038/s41467-020-19344-1 [PubMed]
  • Kazlauskas D, Krupovic M, Guglielmini J, Forterre P, Venclovas Č. (2020) Diversity and evolution of B-family DNA polymerases. Nucleic Acids Research, 48(18):10142–10156. doi: 10.1093/nar/gkaa760 [PubMed]
  • Makarova KS, Timinskas A, Wolf YI, Gussow AB, Šikšnys V, Venclovas Č, Koonin EV. (2020) Evolutionary and functional classification of the CARF domain superfamily, key sensors in prokaryotic antivirus defense. Nucleic Acids Research, 48(16):8828–8847. doi: 10.1093/nar/gkaa635 [PubMed]
  • Makarova KS, Wolf YI, Iranzo J, Shmakov SA, Alkhnbashi OS, Brouns SJJ, Charpentier E, Cheng D, Haft DH, Horvath P, Moineau S, Mojica FJM, Scott D, Shah SA, Šikšnys V, Terns MP, Venclovas Č, White MF, Yakunin AF, Yan W, Zhang F, Garrett RA, Backofen R, van der Oost J, Barrangou R, Koonin EV. (2020) Evolutionary classification of CRISPR-Cas systems: A burst of class 2 and derived variants. Nature Reviews Microbiology, 18(2):67–83. doi: 10.1038/s41579-019-0299-x [PubMed]
  • Timinskas K, Venclovas Č. (2019) New insights into the structures and interactions of bacterial Y-family DNA polymerases. Nucleic Acids Research, 47(9):4393–4405. doi: 10.1093/nar/gkz198 [PubMed]
  • Kazlauskienė M, Kostiuk G, Venclovas Č, Tamulaitis G, Šikšnys V. (2017) A cyclic oligonucleotide signaling pathway in type III CRISPR-Cas systems. Science, 357(6351):605–609. doi: 10.1126/science.aao0100 [PubMed]
  • Olechnovič K, Venclovas Č. (2017) VoroMQA: Assessment of protein structure quality using interatomic contact areas. Proteins, 85(6):1131–1145. doi: 10.1002/prot.25278 [PubMed]
  • Olechnovič K, Kulberkytė E, Venclovas Č. (2013) CAD-score: A new contact area difference-based function for evaluation of protein structural models. Proteins, 81(1):149–162. doi: 10.1002/prot.24172 [PubMed]